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broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/
BSD 3-Clause "New" or "Revised" License
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Conflicting levels of pathogenicity pulling more than it should #84

Closed sambaxter closed 2 years ago

sambaxter commented 2 years ago

The logic for including "Conflicting levels of pathogenicity" should only be when one of the conflicting listings is "pathogenic" or "Likely pathogenic" - right now it is pulling in all conflicting variants.

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nawatts commented 2 years ago

So far as I can tell, I used to think this would require importing ClinVar data from the XML file instead of VCFs. However, it looks like there is a CLNSIGCONF field in the VCFs that can be used for this.